• Home

• Overview

• Publications

• Research

• Software

• NAMD

• VMD

• GPU Computing

• Lattice Microbes

• Atomic Resolution Brownian Dynamics

• MDFF

• QwikMD

• VND (Neuronal)

• Other

• Outreach

NAMD Announcements

• NAMD 2.14 release (8/5/2020)
• NAMD 2.14b2 release (6/25/2020)
• NAMD 2.14b1 release (5/5/2020)

• UD team using supercomputer simulations to analyze the coronavirus (U. Delaware, March 27, 2020)
• Coronavirus Massive Simulations Completed on Frontera Supercomputer (TACC, March 24, 2020)
• Blue Waters aids researchers in breakthrough flu simulations (NCSA, February 25, 2020)
• CAAR Partnerships for Frontier Announced (Oak Ridge Leadership Computing Facility, September 4, 2019)
• New NESAP Teams Start Prepping Applications for Next-Generation Perlmutter Architecture (NERSC, March 27, 2019)

• NAMD 2.13 New Features
• NAMD 2.13 release (11/9/2018)
• NAMD 2.13b2 release (10/16/2018)
• NAMD 2.13b1 release (9/7/2018)
• One-click interactive molecular modeling in the Amazon cloud

• Supercomputing HIV-1 Replication at TACC (Inside HPC, August 10, 2018)
• Team brings subatomic resolution to computational microscope (Illinois News Bureau, Mar 26, 2018)
• ALCF Aurora Early Science Program Now Targeting 2021 Exascale System (Argonne Leadership Computing Facility, January 18, 2018)
• NAMD Aurora Early Science Project (PI: Benoit Roux)

• Enhanced Sampling and Free-Energy Workshop (Urbana, Sept 10-14, 2018)
• NAMD Developer Workshop (Urbana, June 11-12, 2018)
• "Hands-On" Workshop on Computational Biophysics (Pittsburgh, May 21-25, 2018)
• 16th Annual Workshop on Charm++ and its Applications (Urbana, April 11-12, 2018)
• "Hands-On" Workshop on QM/MM Simulation (Urbana, April 5-7, 2018)

• Opening New Frontiers in the Battle Against HIV/AIDS (NVIDIA, September 15, 2017)
• Massive simulation shows HIV capsid interacting with its environment (Illinois News Bureaus, July 19, 2017)
• Assembling Life's Molecular Motor (Oak Ridge Leadership Computing Facility, May 9, 2017)
• Early Science Projects for Aurora Supercomputer Announced (Argonne Leadership Computing Facility, January 30, 2017)

• "Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation (Urbana, September 25-29, 2017)
• "Hands-On" Workshop on Computational Biophysics (Pittsburgh, May 30-June 2, 2017)
• NAMD Developer Workshop (Chicago, May 22-23, 2017)
• 15th Annual Workshop on Charm++ and its Applications (Urbana, April 17-19, 2017)
• "Hands-On" Workshop on Computational Biophysics (Urbana, April 17-21, 2017)
• PRACE Spring School 2017, Sweden - HPC for Life Sciences (Stockholm, April 10-13, 2017)

• QM/MM Interface to MOPAC and ORCA
• QwikMD GUI Released in VMD 1.9.3
• NAMD 2.12 New Features
• NAMD 2.12 release (12/22/2016)
• NAMD 2.12b1 release (11/2/2016)

• 2005 NAMD Reference Paper Has 6,000 Citations (October 6, 2016)
• 2016 User Survey Report (April, 2016)
• Blue Waters simulates largest membrane channel made of DNA origami (NCSA, November 7, 2016)
• Tiny terrors: Researcher works to uncover how bacteria develop antibiotic resistance through efflux pumps (NCSA, May 5, 2016)
• Multiyear simulation study provides breakthrough in membrane protein research (Argonne Leadership Computing Facility, April 5, 2016)
• Blue Waters enables massive flu simulations (NCSA, March 23, 2016)
• Better understanding of voltage-gated-like ion channels may spark improvements in general anesthesia (NCSA, March 16, 2016)
• Study offers clearest picture yet of how HIV defeats a cellular defender (Illinois News Bureau, March 4, 2016)

• "Hands-On" Workshop on Computational Biophysics (San Francisco, December 12-16, 2016)
• "Hands-On" Workshop on Computational Biophysics (Atlanta, November 14-18, 2016)
• "Hands-On" Workshop on Computational Biophysics (Urbana, October 17-21, 2016)
• "Hands-On" Workshop on Computational Biophysics (Jülich, August 15-19, 2016)
• "Hands-On" Workshop on Computational Biophysics (Pittsburgh, June 6-10, 2016)
• NAMD Developer Workshop (Chicago, May 26-27, 2016)
• 14th Annual Workshop on Charm++ and its Applications (Urbana, April 19-20, 2016)

• Researchers resolve structure of a key component of bacterial decision-making (Illinois News Bureau, December 8, 2015)
• TCBG Papers and Presentations at SC15 (November 15-20, 2015)
• Charm++-Related Events at SC15 (November 15-20, 2015)
• TCBG Reaches Milestone 40th Workshop (October 20, 2015)
• 2005 NAMD Reference Paper Has 5000 Citations (October 15, 2015)
• Tajkhorshid Goes After Uncharted Territories in the Molecular World (Beckman Institute, September 28, 2015)
• Beckman Researchers Construct Atomic Model of an Immature Retrovirus (Beckman Institute, August 11, 2015)
• ALCF selects projects for Theta Early Science Program (Argonne Leadership Computing Facility, August 6, 2015)
• Cellulosomes: One of Life's Strongest Biomolecular Bonds Discovered with Use of Supercomputers (Scientific Computing, July 28, 2015)
• OLCF Selects Application Readiness Projects to Prepare for Next-generation Summit Supercomputer (Oak Ridge Leadership Computing Facility, April 15, 2015)
• Supercomputers Help Solve Puzzle-Like Bond for Biofuels (Texas Advanced Computing Center, March 16, 2015)

• NAMD 2.11 New Features
• NAMD 2.11 release (12/22/2105)
• NAMD 2.11b2 release (12/4/2105)
• NAMD 2.11b1 release (11/10/2105)

• "Hands-On" Workshop on Computational Biophysics (Odense, October 12-16, 2015)
• "Hands-On" Workshop on Computational Biophysics (San Diego, September 21-25, 2015)
• "Hands-On" Workshop Using VMD and NAMD (Okazaki, Japan, September 9-11, 2015)
• "Hands-On" Workshop on Computational Biophysics (Berkeley, August 3-7, 2015)
• "Hands-On" Workshop on Computational Biophysics (Pittsburgh, June 1-5, 2015)
• 13th Annual Workshop on Charm++ and its Applications (Urbana, May 7-8, 2015)
• "Hands-On" Workshop on Computational Biophysics (Urbana, April 6-10, 2015)

• Real Science Using Stampede's Xeon Phi (Texas Advanced Computing Center, December 16, 2014)
• Molecules for the Masses: App Puts Chemistry at the Tips of Users' Fingers (Beckman Institute News, December 10, 2014)
• TCBG Papers and Presentations at SC14 (November 16-21, 2014)
• Charm++-Related Events at SC14 (November 16-21, 2014)
• NAMD Powers Molecules by Theodore Gray (November 6, 2014)
• 2005 NAMD Reference Paper Has 4000 Citations (September 5, 2014)
• Bolstering Extreme Scale Computational Biology (HPCwire, July 31, 2014)
• Researchers Win CUDA Achievment Award for Fighting HIV (NVIDIA, March 27, 2014)
• "Computing a Virus" LiveB1G Blue Waters Feature (Big Ten Network, January 13, 2014)

• NAMD 2.10 New Features
• NAMD 2.10 release (12/11/2014)
• NAMD 2.10b2 release (11/15/2014)
• NAMD 2.10b1 release (8/22/2014)

• "Hands-On" Workshop on Computational Biophysics (Atlanta, Nov 3-7, 2014)
• "Hands-On" Workshop on Computational Biophysics (Bremen, June 16-20, 2014)
• 12th Annual Workshop on Charm++ and its Applications (Urbana, April 29-30, 2014)
• Workshop on Cryo-EM Modeling Based on X-ray Crystallography (Urbana, Jan 8-10, 2014)

• Difficult dance steps: Team learns how membrane transporter moves (U. Illinois Press Release, December 2, 2013)
• NCSA Receives Honors in 2013 HPCwire Readers' and Editors' Choice Awards (NCSA, November 18, 2013)
• HPCwire Editors' Choice Award: Best use of HPC in life sciences (HPCwire, November 18, 2013)
• Extreme Computational Biology at SC13: An Interview with Dr. Klaus Schulten (HPCwire, November 18, 2013)
• 2005 NAMD Reference Paper Has 3000 Citations (July 5, 2013)
• Code cracks HIV capsid, opens drug possibilities (Dept. of Energy ASCR Discovery, June 4, 2013)
• Illinois Simulation Software Contributes to Breakthrough in Understanding HIV Capsid (U. Illinois Dept. of Computer Science, May 30, 2013)
• Wit, grit and a supercomputer yield chemical structure of HIV capsid (U. Illinois Press Release, May 24, 2013)
• Poliovirus Simulations on BlueGene/Q (Victorian Infectious Diseases Reference Laboratory, 2013)
• U.S./China team determines structure of virus with Blue Waters (NCSA, January 31, 2013)

• "Hands-On" Workshop on Computational Biophysics (Urbana, Nov 18-22, 2013)
• Workshop on GPU Programming for Molecular Modeling (Urbana, Aug 2-4, 2013)
• "Hands-On" Workshop on Computational Biophysics (Pittsburgh, June 10-14, 2013)
• 11th Annual Workshop on Charm++ and its Applications (Urbana, April 15-16, 2013)

• NAMD 2.9 New Features
• NAMD 2.9 release (4/30/2012)
• NAMD 2.9b3 release (4/6/2012)
• NAMD 2.9b2 release (3/26/2012)
• NAMD 2.9b1 release (3/19/2012)

• Fashioning NAMD: A History of Risk and Reward by Lisa Pollack (August 2012)
• Two Engineering at Illinois professors receive 2012 IEEE Computer Society Sidney Fernbach Award (Engineering at Illinois, October 10, 2012)
• Making history Early results indicate Blue Waters will live up to expectations (NCSA, September 24, 2012)
• Hello Siri, Please Start My Experiment Now (Bio-IT World, April 25, 2012)
• 6 science teams begin using Blue Waters Early Science System (NCSA, March 20, 2012)

• "Hands-On" Workshop on Computational Biophysics (Urbana, October 22-26, 2012)
• In-Residence Training at the Theoretical & Computational Biophysics Group (Urbana, July 16-27, 2012)
• 10th Annual Workshop on Charm++ and its Applications (Urbana, May 7-9, 2012)
• Membrane Protein Structural Dynamics Consortium workshop on Membrane Protein Modeling (Chicago, May 1-2, 2012)
• "Hands-On" Workshop on Computational Biophysics (Urbana, February 11-15, 2012)

• 2011 User Survey Report (9/10/2011)

• Researchers Show How Proteins Help DNA Replicate Past a Damaged Site (Oak Ridge Leadership Computing Facility, November 9, 2011)
• SC11: Scaling to 100 Million Atoms (NCSA Access Online, October 4, 2011)
• How Copper Folds Protein into Parkinson's Plaques (North Carolina State University, June 14, 2011)
• Team solves decades-old molecular mystery linked to blood clotting (University of Illinois, May 31, 2011)
• Researchers get a first look at the mechanics of membrane proteins (University of Illinois, April 18, 2011)

• NAMD 2.8 New Features
• NAMD 2.8 release (5/31/2011)
• NAMD 2.8b3 release (5/19/2011)
• NAMD 2.8b2 release (5/12/2011)
• NAMD 2.8b1 release (3/25/2011)

• Online Workshop on Simulating Membrane Channels (Nov 28-Dec 1, 2011)
• "Hands-On" Workshop on Computational Biophysics (Bremen, October 17-21, 2011)
• Online Workshop on Simulating Membrane Channels (August 1-4, 2011)
• In-Residence Training at the Theoretical & Computational Biophysics Group (Urbana, July 25 - August 5, 2011)
• "Hands-On" Workshop on Computational Biophysics (Pittsburgh, May 16-20, 2011)
• 9th Annual Workshop on Charm++ and its Applications (Urbana, April 18-20, 2011)
• "Hands-On" Workshop on Computational Biophysics (Atlanta, March 21-25, 2011)

• When Cellular Bones Soften (PSC Projects in Scientific Computing, Fall 2010)
• Getting the Rabbit in the Hat (NCSA Access, Summer 2010)
• Insights Into Deafness (NCSA Access, Summer 2010)
• Researcher simulates Alzheimer's 'protein misfolding' errors (Ohio Supercomputer Center, April 21, 2010)
• Supercomputers Simulate the Molecular Machines that Replicate and Repair DNA (ORNL/NCCS, June 2010)
• Sound Science (TACC, June 2010)
• Blueprint for the Affordable Genome (TACC, April 2010)
• Molecular Mechanics of Hearing and Deafness (Harvard MCB, April 2010)
• Structure of inner-ear protein is key to both hearing and inherited deafness (Harvard Medical School, April 2010)
• TeraGrid resources help Harvard team gain insights into deafness (TeraGrid, April 2010)
• 2005 NAMD Reference Paper Has 1000 Citations (March 29, 2010)

• "Hands-On" Workshop on Computational Biophysics (Urbana, Nov 29 - Dec 3, 2010)
• "Hands-On" Workshop on Computational Biophysics (Urbana, Nov 1-5, 2010)
• Workshop on GPU Programming for Molecular Modeling (Urbana, Aug 6-8, 2010)
• "Hands-On" Workshop on Computational Biophysics using NAMD and VMD (Pittsburgh, May 10-14, 2010)
• 8th Annual Workshop on Charm++ and its Applications (Urbana, April 28-30, 2010)

• NAMD 2.7 New Features
• NAMD 2.7 release (10/15/2010)
• NAMD 2.7b4 release (9/17/2010)
• NAMD 2.7b3 release (7/6/2010)
• NAMD 2.7b2 release (11/12/2009)
• NAMD 2.7b1 release (3/23/2009)

• Inside the Swine Flu Virus (TACC, May 2009)
• Closing the Gaps (NCSA, April 2009)

• "Hands-On" Workshops on Computational Biophysics (August 10-14, 2009)
• "Hands-On" Workshops on Computational Biophysics (July 6-10, 2009)
• Charm++ Workshop (April 15-17, 2009)

• TCBG Software at SC08 (November 15-21, 2008)
• Charm++ Workshop (May 1-3, 2008)
• Initial NCSA IACAT Projects to Accelerate NAMD (January 3, 2008)
• Buckyball Bowling with BigBen and Wiimo in Reno (December 4, 2007)
• TCBG Software at SC07 (November 10-16, 2007)
• Charm++ Workshop (April 18-20, 2007)

• Supercomputer Simulations May Pinpoint Causes of Parkinson's, Alzheimer's Diseases (SDSC Press Release, March 19, 2007)
• Knock, Knock, Who's There? (PSC Projects in Scientific Computing, Fall 2006)
• Step Up to the BAR Domain (PSC Projects in Scientific Computing, Fall 2006)

• NAMD 2.6 release (8/31/2006)
• NAMD 2.6b2 release (8/17/2006)
• NAMD 2.6b1 release (7/30/2005)

• Protein Wranglers (NCSA Access, Summer 2006)
• TCBG Software at SC2006 (November 13-16, 2006)
• Virus Simulated on SGI Altix (SGI Press Release, May 10, 2006)
• Managing Workflow with NAMD-G (NCSA Data Link, April 2006)

• Cluster-Building Workshop, November 30 - December 1, 2006
• Cluster-Building Workshops, March 16-17 and April 20-21, 2006
• Cluster-Building Workshops, Sept 22-23 and Nov 10-11, 2005

• 2005 Survey Report

• Enzyme Antics (NCSA Access, Fall 2005)
• All in Your Brain (PSC Projects in Scientific Computing, Fall 2005)
• NAMD/VMD-based SPICE wins the HPC Analytics Challenge Award at SC|05
• TCBG Software at SC2005 (November 14-17, 2005)
• Charm++ Workshop, Oct 17-19, 2005
• Understanding the Protein Lock (NCSA Access, Spring 2005)

• Frankfurt Hands-On Workshop, March 20-23, 2006
• Pittsburgh Hands-On Workshop, Nov 28-Dec 1, 2005
• San Francisco Hands-On Workshop, June 26-30, 2005
• Chicago Hands-On Workshop, June 9-13, 2005
• Tahoe Hands-On Workshop, May 23-27, 2005
• Boston Hands-On Workshop, Dec 5-9, 2004
• Urbana Hands-On Workshop, Nov 8-12, 2004

• Mechanosensitive Ion Channels (NCSA Access, 12/1/2004)
• TCBG Software at SC2004 (November 8-11, 2004)
• Charm++ Workshop, Oct 18-20, 2004
• FlashMob 2004 Uses NAMD (8/25/2004)

• TCBG Software at SC2003 (November 17-20, 2003)
• Protein Border Guards (PSC In Progress, 10/2003)

• NAMD 2.5 release (9/29/2003)
• NAMD 2.5b3 release (9/19/2003)
• NAMD 2.5b2 release (9/15/2003)

• Summer School on Theoretical and Computational Biophysics, June 2-13, 2003 (notes available)

• 2003 Survey Report

• NAMD Breaks Tflop/s Barrier (12/19/2002)
• PSC's LeMieux Enables Award-Winning Science (PSC Press Release, 12/5/2002)
• NAMD Wins Gordon Bell Award (UIUC Press Release, 12/4/2002)
• SC2002 Gordon Bell Awards (SC2002 Press Release, 11/21/2002)
• NAMD and VMD at SC2002 (November 18-22, 2002)
• SC2002 Gordon Bell Award Finalists (SC2002 Press Release, 11/7/2002)

• NAMD 2.5b1 release (4/18/2002)
• NCSA NAMD Workshop April 17-19, 2002 (notes available)

• Precious Bodily Fluids (PSC Feature, 9/30/2002)
• How Proteins Filter Water (PSC News Center, 4/22/2002)

• NAMD 2.4 release (3/11/2002)
• NAMD 2.4b2 release (2/22/2002)
• NAMD 2.4b1 release (1/25/2002)

• NAMD and VMD at SC2001 (November 12-15, 2001)
• VMD with NAMD, JMV, and BioCoRE at Siggraph 2001 (August 14-16, 2001)

• Molecular Dynamics Workshop at PSC, August 15-18, 2001 (notes available)
• Linux Cluster Tutorial at NCSA, June 25, 2001 (notes available)

• Modeling ATP (NCSA Access, 10/9/2001)
• Touchy Proteins (PSC Feature, 9/17/2001)
• The Road to La-La Land (PSC Feature, 7/27/2001)
• The Rude Mechanicals (PSC Feature, 6/27/2000)

• NCSA Itanium Cluster Press Release featuring NAMD (10/18/2001)
• Scyld Press Release (1/29/2001)
• PSC Terascale Press Release citing NAMD benchmarks (1/29/2001)

• NAMD 2.3 release (8/2/2001)
• NAMD 2.3b2 release (7/2/2001)
• NAMD 2.3b1 release (2/23/2001)

• NAMD 2.2 release (9/29/2000)
• NAMD 2.2b3 release (9/25/2000)
• NAMD 2.2b2 release (9/15/2000)
• NAMD 2.2b1 release (9/5/2000)

• Survey 2000 statistical findings and responses

• NAMD 2.1 release (11/11/1999)
• NAMD 2.1b4 release (10/29/1999)
• NAMD 2.1b3 release (10/25/1999)
• NAMD 2.1b2 release (10/8/1999)
• NAMD 2.1b1 release (9/15/1999)

• NAMD 2.0 release (3/25/1999)
• NAMD 2.0b3 release (2/26/1999)
• NAMD 2.0b2 release (10/16/1998)

• NAMD 1.5 release (9/4/1998)